This is how I work, too, only I'm converting to epub for my Nook ( I like to try to keep the art and dividers within the fic, if it's at all feasible).

I don't know if anyone else does this, but for single file fics I like the Safari Reader, which gives you just the text, cuts off comments, etc. and lets you save fic as a pdf directly to the desktop (or wherever) - convert in calibre and voila. It's especially nice for Dreamwidth, since it eliminates the LJ character limit problem. : )